← home · ← tools · View as Markdown (.md) · JSON

get-structure

station__rcsb-org__get-structure external (needs EXECUTION_BACKEND_URL) rcsb-org pv-adjacent Constructa Configa

Fetch full PDB structure (atom coordinates + metadata) for a given PDB ID. Returns raw PDB text plus parsed metadata (chains, ligands, resolution). Use for client-side 3D rendering of the receptor-ligand complex.

Taxonomy

Linnaean classification joined from the algovigilance taxonomy index via the parent config's rank.

Rank	Value
domain	`Substrata`
kingdom	`Constructa`
phylum	`Configa`
class	`station-config`
order	`rcsb_pdb`
family	`mcp-tool-config`

Characteristics:

substrate: config
domain: pv
lifecycle: continuous
authority: read
compounding: producer
io: agent-request → tool-response

Input schema

pdb_id stringrequired — 4-character PDB identifier (e.g., '3RFM')
include_coords boolean — Include raw PDB file text (default true). Set false for metadata-only response.

Example call

POST /api/mcp
Content-Type: application/json

{
  "jsonrpc": "2.0",
  "id": 1,
  "method": "tools/call",
  "params": {
    "name": "station__rcsb-org__get-structure",
    "arguments": {
      "pdb_id": ""
    }
  }
}

How to invoke from a client

From any MCP-aware client, add https://algovigilance.com/api/mcp as an MCP server, then call this tool by name. From a raw HTTP client, send the JSON-RPC body above to /api/mcp.

Agent-friendly formats

Working inside an AI assistant? Use the Copy for AI button at the top of this page (or view the raw Markdown) to paste a clean, token-budgeted version of this tool's contract into your conversation.

All tools (3062 live)
/api/mcp — endpoint
/AGENTS.md — agent guide
/tools/rcsb-org__get-structure/raw.md — this page's Markdown twin